Results

Below you find for each supplied fasta file an individual tab. Each tab contains all the results and explanations to help you identify the possible phages.
The results are also grouped by blue tabs. All the citations can be found in the results directory as a .bib file

ERR575691_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

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CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

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ERR575692_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

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CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

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ERR576942_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

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CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

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ERR576943_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

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CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

Back to top

ERR576944_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

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CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

Back to top

ERR576945_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

Back to top


CheckV output


Tab. 1: CheckV output


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Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

Back to top

ERR576946_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

Back to top


CheckV output


Tab. 1: CheckV output


Back to top


Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

Back to top

ERR579308_raw_assembly


Overview


Performance of each identification tool


Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).

How to read this plot

The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.

Back to top


Phage annotations


Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database

tax classification

contig prediction_value predicted_organism_name

ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome

Back to top


CheckV output


Tab. 1: CheckV output


Back to top


Phage prediction by contig


Phage prediction table

Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.

Explanation tool output

Tab.2: The output of each tool and what WtP puts in Tab. 1.

Tool Standard output WtP displayed value
deepvirfinder p-value: 0 to 1 0 to 1
metaphinder string: phage 1
metaphinder own string: phage 1
phigaro score: 0 to 1 0 to 1
pprmeta phage_score: 0 to 1 0 to 1
seeker score: 0 to 1 0 to 1
sourmash similarity: 0 to 1 0 to 1
vibrant prediction: virus 1
vibrant-virome prediction: virus 1
virfinder p-value: 0 to 1 0 to 1
virnet score: 0 to 1 0 to 1
virsorter category 1, category 2, category 3 1, 0.5, 0
virsorter-virome category 1, category 2, category 3 1, 0.5, 0
virsorter2 dsDNAphage: 0 to 1 0 to 1

How to extract contigs of interest

  1. Choose/filter for the contigs of interest in Table 1.
  2. Export and download the table as a .csv file
  3. Execute the the following bash commands to extract the desired contigs from your .fasta
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
    hier kommt noch was
    oranage: #F79A30
    pink    #E35E9F
    lila    #8F2ABF
done 

Back to top


Taxonomic Phage classification


Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.


hier nochn satz was der wert ist probability

Back to top